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- PDB-7pi2: PfCyRPA bound to monoclonal antibody Cy.003 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7pi2
TitlePfCyRPA bound to monoclonal antibody Cy.003 Fab fragment
Components
  • Cysteine-rich protective antigen
  • Monoclonal antibody Cy.003 heavy chain
  • Monoclonal antibody Cy.003 light chain
KeywordsIMMUNE SYSTEM / malaria / Plasmodium falciparum / monoclonal antibody / vaccine
Function / homology
Function and homology information


microneme lumen / microneme / symbiont entry into host / apical part of cell / cytoplasmic vesicle / host extracellular space / host cell plasma membrane / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Cysteine-rich protective antigen 6 bladed domain / Cysteine-Rich Protective Antigen 6 bladed domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cysteine-rich protective antigen
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsRagotte, R.J. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Heterotypic interactions drive antibody synergy against a malaria vaccine candidate.
Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / ...Authors: Ragotte, R.J. / Pulido, D. / Lias, A.M. / Quinkert, D. / Alanine, D.G.W. / Jamwal, A. / Davies, H. / Nacer, A. / Lowe, E.D. / Grime, G.W. / Illingworth, J.J. / Donat, R.F. / Garman, E.F. / Bowyer, P.W. / Higgins, M.K. / Draper, S.J.
History
DepositionAug 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.003 heavy chain
C: Monoclonal antibody Cy.003 light chain
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.003 heavy chain
F: Monoclonal antibody Cy.003 light chain
G: Cysteine-rich protective antigen
H: Monoclonal antibody Cy.003 heavy chain
I: Monoclonal antibody Cy.003 light chain
J: Cysteine-rich protective antigen
K: Monoclonal antibody Cy.003 heavy chain
L: Monoclonal antibody Cy.003 light chain


Theoretical massNumber of molelcules
Total (without water)345,93312
Polymers345,93312
Non-polymers00
Water00
1
A: Cysteine-rich protective antigen
B: Monoclonal antibody Cy.003 heavy chain
C: Monoclonal antibody Cy.003 light chain


Theoretical massNumber of molelcules
Total (without water)86,4833
Polymers86,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Cysteine-rich protective antigen
E: Monoclonal antibody Cy.003 heavy chain
F: Monoclonal antibody Cy.003 light chain


Theoretical massNumber of molelcules
Total (without water)86,4833
Polymers86,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Cysteine-rich protective antigen
H: Monoclonal antibody Cy.003 heavy chain
I: Monoclonal antibody Cy.003 light chain


Theoretical massNumber of molelcules
Total (without water)86,4833
Polymers86,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Cysteine-rich protective antigen
K: Monoclonal antibody Cy.003 heavy chain
L: Monoclonal antibody Cy.003 light chain


Theoretical massNumber of molelcules
Total (without water)86,4833
Polymers86,4833
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)354.300, 71.045, 164.789
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cysteine-rich protective antigen / Inactive sialidase CyRPA


Mass: 40184.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: CyRPA, pfd1130w, PF3D7_0423800 / Production host: Homo sapiens (human) / References: UniProt: Q8IFM8
#2: Antibody
Monoclonal antibody Cy.003 heavy chain


Mass: 23926.654 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
#3: Antibody
Monoclonal antibody Cy.003 light chain


Mass: 22372.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M MES pH 6, 20 % PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.14→164.76 Å / Num. obs: 239064 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.956 / Net I/σ(I): 7.2
Reflection shellResolution: 3.14→3.21 Å / Num. unique obs: 15017 / CC1/2: 0.425

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TIH

5tih


Resolution: 3.14→88.56 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.856 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 3461 4.78 %RANDOM
Rwork0.2187 ---
obs0.2197 72368 99.8 %-
Displacement parametersBiso max: 225.04 Å2 / Biso mean: 89.83 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-14.4935 Å20 Å2-0.4423 Å2
2---28.9359 Å20 Å2
3---14.4424 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 3.14→88.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23353 0 0 0 23353
Num. residues----3002
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8064SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4045HARMONIC5
X-RAY DIFFRACTIONt_it23907HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3128SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16018SEMIHARMONIC0
X-RAY DIFFRACTIONt_bond_d23907HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg32426HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion19.74
LS refinement shellResolution: 3.14→3.16 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3145 60 4.14 %
Rwork0.2689 1388 -
all-1448 -
obs--99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.15840.14341.12311.52280.35241.9325-0.26690.54360.39460.2097-0.02170.0351-0.1260.03640.28860.0198-0.0853-0.15310.01960.07490.0675-24.8739-25.261617.0453
21.74660.00021.72090.7202-0.65142.3226-0.07130.18880.132-0.0849-0.19310.0880.05950.47190.26440.0372-0.01470.05010.28970.0203-0.003714.5698-40.84648.6858
31.54840.20911.24810.29910.16061.8412-0.0917-0.45560.15850.0313-0.19450.2672-0.1484-0.04440.28620.1267-0.03310.11580.2958-0.0688-0.02816.4898-38.306965.322
43.5702-0.4248-1.02671.43010.3031.8817-0.1323-0.5398-0.2428-0.23260.05030.15270.29770.09120.08190.12060.05740.0184-0.09130.01160.1289-25.7778-74.524164.2015
52.00930.4792-2.49730.4477-1.35493.1099-0.0608-0.16390.0928-0.2278-0.08880.28280.18210.54110.14960.21580.15090.01270.3040.0574-0.074214.7914-58.790734.4829
62.34690.8287-2.94931.1292-0.55774.1567-0.2065-0.0368-0.1819-0.3792-0.12290.44410.43730.52550.32940.30980.1522-0.13960.1827-0.0099-0.30987.6288-61.323417.5567
73.77270.5965-0.56041.32680.11451.1246-0.23410.5207-0.01760.02350.2513-0.1423-0.0006-0.0878-0.01710.0392-0.0980.0910.2881-0.0877-0.1053106.7229-10.1287.1341
81.59580.8377-1.37890.6039-0.50952.2625-0.00210.19220.090.03310.17590.1169-0.0522-0.1463-0.17380.0974-0.01940.01680.19180.04930.041265.4352-19.673438.2141
92.91821.497-1.62040.8617-0.73651.4174-0.1707-0.0489-0.2704-0.01660.1385-0.1780.0516-0.07450.03220.0813-0.00690.03080.16620.05790.096271.044-35.158745.8759
103.6798-1.05750.73791.4777-0.02381.478-0.1793-0.5403-0.2489-0.03330.2316-0.1612-0.0667-0.2021-0.0523-0.07520.0431-0.02890.3040.0607-0.1041107.0712-86.244273.8629
111.9749-1.36930.97741.8911-1.28571.2880.0934-0.2512-0.0979-0.31410.06460.06570.0922-0.099-0.1580.15610.04040.02190.2047-0.0486-0.050167.1606-69.582142.7342
121.7115-1.36281.42441.5015-0.88071.5671-0.1842-0.0166-0.0323-0.09320.1497-0.265-0.4710.00480.03450.30440.0242-0.00610.12490.0063-0.08975.6963-55.328535.3317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|361 }A31 - 361
2X-RAY DIFFRACTION2{ B|20 - B|246 }B20 - 246
3X-RAY DIFFRACTION3{ C|23 - C|230 }C23 - 230
4X-RAY DIFFRACTION4{ D|31 - D|361 }D31 - 361
5X-RAY DIFFRACTION5{ E|20 - E|245 }E20 - 245
6X-RAY DIFFRACTION6{ F|23 - F|229 }F23 - 229
7X-RAY DIFFRACTION7{ G|31 - G|361 }G31 - 361
8X-RAY DIFFRACTION8{ H|20 - H|247 }H20 - 247
9X-RAY DIFFRACTION9{ I|23 - I|230 }I23 - 230
10X-RAY DIFFRACTION10{ J|31 - J|361 }J31 - 361
11X-RAY DIFFRACTION11{ K|20 - K|247 }K20 - 247
12X-RAY DIFFRACTION12{ L|23 - L|229 }L23 - 229

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